I am having a similar issue with AA and US and add in a travel agent and the fact that it is ticketed by BA and subtract the award ticket part.

I also had similar weirdness with duplicate flights booked and different itineraries showing up on different airlines websites. I got the same answer from US Air that since my original itinerary had 2 stops they could only change it to an itinerary with 2 stops. I have had both nice agents who seemed to try but weren't able to help and absolutely awful ones that were rude, condescending and told me things that were obviously wrong.

I got them to put me on flights that have legal connection times (though not what I was hoping for), but in changing the flights I now have US Air flight numbers for which which US Air says I am not ticketed. The flights are operated by AA who does say that I am ticketed. Hard to know who to trust.

One US agent told me there were "big" schedule changes coming this weekend, so maybe wait a couple of days to see what happens?

No answers, just commiseration, and I wish you good luck and helpful agents!